阿拉伯芥古氏基因啟動子研究分析與植物啟動子分析平台暨生物資料庫之建構 ; Promoter analysis of Ku genes from Arabidopsis and construction of novel web server and database for plant promoter analysis

التفاصيل البيبلوغرافية
العنوان: 阿拉伯芥古氏基因啟動子研究分析與植物啟動子分析平台暨生物資料庫之建構 ; Promoter analysis of Ku genes from Arabidopsis and construction of novel web server and database for plant promoter analysis
المؤلفون: 張文綺, Wen-Chi Chang
المساهمون: 潘榮隆, 黃憲達, Rong-Long Pan, Hsien-Da Huang
سنة النشر: 2008
المجموعة: National Tsing Hua University Institutional Repository (NTHUR)
مصطلحات موضوعية: 啟動子, 阿拉伯芥, 古氏基因, 基因調控, 轉錄因子, promoter, Arabidopsis, Ku gene, gene regulation, transcription factor
الوقت: 35
الوصف: 博士 ; 國立清華大學 ; 生物資訊與結構生物研究所 ; GH000928204 ; 啟動子在基因表現的調控上扮演極重要的角色。在本論文中,我們使用in vivo 和in silico的方法來研究植物的啟動子。除了用實驗的方法分析阿拉伯芥古氏基因(AtKu70 和AtKu80)啟動子外,也建立一以資料庫為輔的植物啟動子分析網路服務平台。 第一部份,我們以轉殖阿拉伯芥來研究阿拉伯芥古氏基因(AtKu70 和AtKu80)的啟動子活性。在高等植物中,阿拉伯芥古氏基因在DNA 修復的非同源末端結合(non-homologous endjoining)機制中扮演極重要的角色。阿拉伯芥古氏基因在植物系統與在哺乳類動物系統一樣都具有多重細胞功能,例如:參與維持染色體端粒(telomere)長度、參與轉錄過程、參與細胞凋亡(apotosis)等。然而,在哺乳動物中會持續性地表現大量的古氏基因,但相對之下,在高等植物中,古氏基因的表現量低。在本研究中,我們想要瞭解阿拉伯芥古氏基因在高等植物中是如何被調控的。因此我們選殖出阿拉伯芥古氏基因的啟動子區域,再接上GUS 報導基因,然後利用轉殖植物來研究該啟動子的活性。我們發現,在植物發育初期,阿拉伯芥古氏基因啟動子在下胚軸和子葉具有很高的活性,另外,在花與果莢發育初期,花的柱頭和果莢也都有較高的啟動子活性。另一方面,我們也發現吉貝素(gibberellic acid)、植物生長激素(auxins)和茉莉酸(jasmonic acid)會促進阿拉伯芥古氏基因啟動子活性;相反地,離酸(abscisic acid)、水楊酸(salicylic acid)、 熱逆境、乾旱逆境和冷逆境都會抑制阿拉伯芥古氏基因啟動子活性。除此之外,我們利用片段分析(deletion analysis)發現AtKu70 的最小功能啟動子區域約在轉錄起始點(transcription start site)上游約400 鹼基對的位置,而AtKu80 則在600 鹼基對的位置。綜合以上,我們發現阿拉伯芥古氏基因的調控與植物發育相關,同時,也受到植物賀爾蒙與環境逆境的影響。 第二部分,隨著許多植物基因體定序計畫的完成,例如:阿拉伯芥、稻米和玉米等,快速有效地研究植物基因轉錄的調控在植物科學中便是一非常重要的課題。目前已有許多關於植物啟動子的生物資訊服務平台和資料庫被開發出來,但他們多只著重於註解單一基因啟動子之轉錄因子結合位置,而忽略了啟動子上其他重要的調控因子,例如:串連的重複區域(tandem repeats) 和CpG/CpNpG 島 (CpG/CpNpG islands)。另一方面,組合的轉錄因子在調控一群表現情況類似的基因是非常重要的。因此,我們便想開發一工具用來分析調控一群基因啟動子的組合轉錄因子(combinatorial transcription factors)。在本研究中,我們建構一資料庫輔助的網路服務平台—PlantPAN (Plant Promoter Analysis Navigator),本系統除可辨識出一群共同表現基因啟動子上之組合的近端調控因子(combinatorial cis-regulatory elements)外,同時還考慮組合轉錄因子之間的距離是否在合理範圍內。本系統所收集的植物轉錄因子主要是來自TRANSFAC、PLACE、AGRIS 和JASPER 四個資料庫,使用本系統分析組合轉錄因子時,使用者可輸入一群基因識別碼(Gene IDs)或啟動子序列,透過本系統的分析,在這一群基因啟動子上同時出現的組合轉錄因子結合位置便會被辨識出來,同時可限制組合的轉錄因子之間的距離在20 到200 鹼基對之間。除了轉錄因子結合位置的分析外,本系統也提供註解植物啟動子上串連重複區域和CpG/CpNpG 島。為使本系統更臻完善,同源基因啟動子保留區域(conserved regions)中的調控因子也可透過本系統被偵測及標示出來。另一方面,由於最近很多研究發現microRNA 在基因表現的調控上也扮演很重要的角色,因此在PlantPAN 中,我們特別發展一工具來辨識microRNA在傳訊RNA (mRNA)和5’端未轉譯區域 (5’UTR) 的標的結合位置。本新開發的系統目前已可在http://PlantPAN.mbc.nctu.edu.twTest 免費使用。 ; Promoter is essential to gene expression regulation. In this study, in vivo and in silico methods were used to analyze plant promoters. In addition to experimental techniques used for investigating AtKu promoter, a ...
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العلاقة: Abe, H., Yamaguchi-Shinozaki, K., Urao, T., Iwasaki, T., Hosokawa, D., and Shinozaki, K. (1997). Role of arabidopsis MYC and MYB homologs in drought- and abscisic acid-regulated gene expression. Plant Cell 9, 1859-1868. Abeel, T., Saeys, Y., Bonnet, E., Rouze, P., and Van de Peer, Y. (2008). Generic eukaryotic core promoter prediction using structural features of DNA. Genome Res 18, 310-323. Balaji, S., Babu, M.M., Iyer, L.M., Luscombe, N.M., and Aravind, L. (2006). Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast. J Mol Biol 360, 213-227. Barrett, T., and Edgar, R. (2006a). Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. Methods Enzymol 411, 352-369. Barrett, T., and Edgar, R. (2006b). Mining microarray data at NCBI's Gene Expression Omnibus (GEO)*. Methods Mol Biol 338, 175-190. Bechtold, N., and Pelletier, G. (1998). In planta Agrobacterium-mediated transformation of adult Arabidopsis thaliana plants by vacuum infiltration. Methods Mol Biol 82, 259-266. Beck, B.D., and Dynlacht, J.R. (2001). Heat-induced aggregation of XRCC5 (Ku80) in nontolerant and thermotolerant cells. Radiat Res 156, 767-774. Bender, J. (2004). DNA methylation and epigenetics. Annu Rev Plant Biol 55, 41-68. Benson, G. (1999). Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27, 573-580. Bertuch, A., and Lundblad, V. (1998). Telomeres and double-strand breaks: trying to make ends meet. Trends Cell Biol 8, 339-342. Boyko, A., Zemp, F., Filkowski, J., and Kovalchuk, I. (2006). Double-strand break repair in plants is developmentally regulated. Plant Physiol 141, 488-497. Brown, A.P., Dunn, M.A., Goddard, N.J., and Hughes, M.A. (2001). Identification of a novel low-temperature-response element in the promoter of the barley (Hordeum vulgare L) gene blt101.1. Planta 213, 770-780. Bryne, J.C., Valen, E., Tang, M.H., Marstrand, T., Winther, O., da Piedade, I., Krogh, A., Lenhard, B., and Sandelin, A. (2008). JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Res 36, D102-106. Bulow, L., Schindler, M., and Hehl, R. (2007). PathoPlant: a platform for microarray expression data to analyze co-regulated genes involved in plant defense responses. Nucleic Acids Res 35, D841-845. Bundock, P., van Attikum, H., and Hooykaas, P. (2002). Increased telomere length and hypersensitivity to DNA damaging agents in an Arabidopsis KU70 mutant. Nucleic Acids Res 30, 3395-3400. Burges, C.J.C. (1998). A Tutorial on Support Vector Machines for Pattern Recognition. Data Mining and Knowledge Discovery 2, 121-127. CAMBIA. (http://www.cambia.orgTest/). Cao, X., and Jacobsen, S.E. (2002). Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proc Natl Acad Sci U S A 99 Suppl 4, 16491-16498. Chang, W.C., Lee, T.Y., Huang, H.D., Huang, H.Y., and Pan, R.L. (2008). PlantPAN: Plant Promoter Analysis Navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene group. unpublish. Chawade, A., Brautigam, M., Lindlof, A., Olsson, O., and Olsson, B. (2007). Putative cold acclimation pathways in Arabidopsis thaliana identified by a combined analysis of mRNA co-expression patterns, promoter motifs and transcription factors. BMC Genomics 8, 304. Craigon, D.J., James, N., Okyere, J., Higgins, J., Jotham, J., and May, S. (2004). NASCArrays: a repository for microarray data generated by NASC's transcriptomics service. Nucleic Acids Res 32, D575-577. Crowe, A.J., Abenes, M., Plant, A., and Moloney, M.M. (2000). The seed-specific transactivator, ABI3, induces oleosin gene expression. Plant Science 151, 171-181. Davuluri, R.V., and Zhang, M.Q. (2003). Computer software to find genes in plant genomic DNA. Methods Mol Biol 236, 87-108. Davuluri, R.V., Sun, H., Palaniswamy, S.K., Matthews, N., Molina, C., Kurtz, M., and Grotewold, E. (2003). AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. BMC Bioinformatics 4, 25. Diaz-De-Leon, F., Klotz, K.L., and Lagrimini, L.M. (1993). Nucleotide sequence of the tobacco (Nicotiana tabacum) anionic peroxidase gene. Plant Physiol 101, 1117-1118. Donald, R.G., and Cashmore, A.R. (1990). Mutation of either G box or I box sequences profoundly affects expression from the Arabidopsis rbcS-1A promoter. Embo J 9, 1717-1726. Dong, X. (1998). SA, JA, ethylene, and disease resistance in plants. Curr Opin Plant Biol 1, 316-323. Featherstone, C., and Jackson, S.P. (1999). Ku, a DNA repair protein with multiple cellular functions? Mutat Res 434, 3-15. Francoeur, A.M., Peebles, C.L., Gompper, P.T., and Tan, E.M. (1986). Identification of Ki (Ku, p70/p80) autoantigens and analysis of anti-Ki autoantibody reactivity. J Immunol 136, 1648-1653. Friesner, J., and Britt, A.B. (2003). Ku80- and DNA ligase IV-deficient plants are sensitive to ionizing radiation and defective in T-DNA integration. Plant J 34, 427-440. Gallego, M.E., Jalut, N., and White, C.I. (2003a). Telomerase dependence of telomere lengthening in Ku80 mutant Arabidopsis. Plant Cell 15, 782-789. Gallego, M.E., Bleuyard, J.Y., Daoudal-Cotterell, S., Jallut, N., and White, C.I. (2003b). Ku80 plays a role in non-homologous recombination but is not required for T-DNA integration in Arabidopsis. Plant J 35, 557-565. Galuschka, C., Schindler, M., Bulow, L., and Hehl, R. (2007). AthaMap web tools for the analysis and identification of co-regulated genes. Nucleic Acids Res 35, D857-862. Gao, G., Zhong, Y., Guo, A., Zhu, Q., Tang, W., Zheng, W., Gu, X., Wei, L., and Luo, J. (2006). DRTF: a database of rice transcription factors. Bioinformatics 22, 1286-1287. Goda, H., Sasaki, E., Akiyama, K., Maruyama-Nakashita, A., Nakabayashi, K., Li, W., Ogawa, M., Yamauchi, Y., Preston, J., Aoki, K., Kiba, T., Takatsuto, S., Fujioka, S., Asami, T., Nakano, T., Kato, H., Mizuno, T., Sakakibara, H., Yamaguchi, S., Nambara, E., Kamiya, Y., Takahashi, H., Hirai, M.Y., Sakurai, T., Shinozaki, K., Saito, K., Yoshida, S., and Shimada, Y. (2008). The AtGenExpress hormone- and chemical-treatment data set: Experimental design, data evaluation, model data analysis, and data access. Plant J. Gong, W., Shen, Y.P., Ma, L.G., Pan, Y., Du, Y.L., Wang, D.H., Yang, J.Y., Hu, L.D., Liu, X.F., Dong, C.X., Ma, L., Chen, Y.H., Yang, X.Y., Gao, Y., Zhu, D., Tan, X., Mu, J.Y., Zhang, D.B., Liu, Y.L., Dinesh-Kumar, S.P., Li, Y., Wang, X.P., Gu, H.Y., Qu, L.J., Bai, S.N., Lu, Y.T., Li, J.Y., Zhao, J.D., Zuo, J., Huang, H., Deng, X.W., and Zhu, Y.X. (2004). Genome-wide ORFeome cloning and analysis of Arabidopsis transcription factor genes. Plant Physiol 135, 773-782. Guo, A., He, K., Liu, D., Bai, S., Gu, X., Wei, L., and Luo, J. (2005). DATF: a database of Arabidopsis transcription factors. Bioinformatics 21, 2568-2569. Guo, A.Y., Chen, X., Gao, G., Zhang, H., Zhu, Q.H., Liu, X.C., Zhong, Y.F., Gu, X., He, K., and Luo, J. (2008). PlantTFDB: a comprehensive plant transcription factor database. Nucleic Acids Res 36, D966-969. Hardtke, C.S., Dorcey, E., Osmont, K.S., and Sibout, R. (2007). Phytohormone collaboration: zooming in on auxin-brassinosteroid interactions. Trends Cell Biol 17, 485-492. Higo, K., Ugawa, Y., Iwamoto, M., and Korenaga, T. (1999). Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res 27, 297-300. Hoffman, M., and Zhang, M.Q. (unpublished). AtProbe: Arabidopsis thaliana Promoter Binding Element Database. http://exon.cshl.org/cgi-bin/atprobe/atprobe.plTest. Huang, H.D., Horng, J.T., Chang, C.H., Tsou, T.S., Hong, J.Y., and Liu, B.J. (2004). A computational approach to discover differential cooperation of regulatory sites in functionally related genes in yeast genome. Journal of Information Science and Engineering 20, 1141-1159 Jaiswal, P., Ni, J., Yap, I., Ware, D., Spooner, W., Youens-Clark, K., Ren, L., Liang, C., Zhao, W., Ratnapu, K., Faga, B., Canaran, P., Fogleman, M., Hebbard, C., Avraham, S., Schmidt, S., Casstevens, T.M., Buckler, E.S., Stein, L., and McCouch, S. (2006). Gramene: a bird's eye view of cereal genomes. Nucleic Acids Res 34, D717-723. Jeddeloh, J.A., Bender, J., and Richards, E.J. (1998). The DNA methylation locus DDM1 is required for maintenance of gene silencing in Arabidopsis. Genes Dev 12, 1714-1725. Jefferson, R.A., Kavanagh, T.A., and Bevan, M.W. (1987). GUS fusions: beta-glucuronidase as a sensitive and versatile gene fusion marker in higher plants. Embo J 6, 3901-3907. Jen, C.-H., Manfield, I.W., Michalopoulos, I., Pinney, J.W., Willats, W.G.T., Gilmartin, P.M., and Westhead, D.R. (2006). The Arabidopsis co-expression tool (act): a WWW-based tool and database for microarray-based gene expression analysis. The Plant Journal 46, 336. Kato, M., Hata, N., Banerjee, N., Futcher, B., and Zhang, M.Q. (2004). Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biol 5, R56. Kel, A.E., Gossling, E., Reuter, I., Cheremushkin, E., Kel-Margoulis, O.V., and Wingender, E. (2003). MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res 31, 3576-3579. Kilian, J., Whitehead, D., Horak, J., Wanke, D., Weinl, S., Batistic, O., D'Angelo, C., Bornberg-Bauer, E., Kudla, J., and Harter, K. (2007). The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J 50, 347-363. Kooter, J.M., Matzke, M.A., and Meyer, P. (1999). Listening to the silent genes: transgene silencing, gene regulation and pathogen control. Trends Plant Sci 4, 340-347. Lescot, M., Dehais, P., Thijs, G., Marchal, K., Moreau, Y., Van de Peer, Y., Rouze, P., and Rombauts, S. (2002). PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res 30, 325-327. Li, G.C., He, F., Shao, X., Urano, M., Shen, L., Kim, D., Borrelli, M., Leibel, S.A., Gutin, P.H., and Ling, C.C. (2003). Adenovirus-mediated heat-activated antisense Ku70 expression radiosensitizes tumor cells in vitro and in vivo. Cancer Res 63, 3268-3274. Lindroth, A.M., Cao, X., Jackson, J.P., Zilberman, D., McCallum, C.M., Henikoff, S., and Jacobsen, S.E. (2001). Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292, 2077-2080. Liu, P.F., Chang, W.C., Wang, Y.K., Chang, H.Y., and Pan, R.L. (2008). Signaling pathways mediating the suppression of Arabidopsis thaliana Ku gene expression by abscisic acid. Biochim Biophys Acta 1779, 164-174. Liu, P.F., Chang, W.C., Wang, Y.K., Munisamy, S.B., Hsu, S.H., Chang, H.Y., Wu, S.H., and Pan, R.L. (2007). Differential regulation of Ku gene expression in etiolated mung bean hypocotyls by auxins. Biochim Biophys Acta 1769, 443-454. Lu, P.L., Chen, N.Z., An, R., Su, Z., Qi, B.S., Ren, F., Chen, J., and Wang, X.C. (2007). A novel drought-inducible gene, ATAF1, encodes a NAC family protein that negatively regulates the expression of stress-responsive genes in Arabidopsis. Plant Mol Biol 63, 289-305. Ludwig, D.L., Chen, F., Peterson, S.R., Nussenzweig, A., Li, G.C., and Chen, D.J. (1997). Ku80 gene expression is Sp1-dependent and sensitive to CpG methylation within a novel cis element. Gene 199, 181-194. Martin, C., Prescott, A., Mackay, S., Bartlett, J., and Vrijlandt, E. (1991). Control of anthocyanin biosynthesis in flowers of Antirrhinum majus. Plant J 1, 37-49. Matys, V., Kel-Margoulis, O.V., Fricke, E., Liebich, I., Land, S., Barre-Dirrie, A., Reuter, I., Chekmenev, D., Krull, M., Hornischer, K., Voss, N., Stegmaier, P., Lewicki-Potapov, B., Saxel, H., Kel, A.E., and Wingender, E. (2006). TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res 34, D108-110. McGinnis, S., and Madden, T.L. (2004). BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res 32, W20-25. Mena, M., Cejudo, F.J., Isabel-Lamoneda, I., and Carbonero, P. (2002). A role for the DOF transcription factor BPBF in the regulation of gibberellin-responsive genes in barley aleurone. Plant Physiol 130, 111-119. Mimori, T., and Hardin, J.A. (1986). Mechanism of interaction between Ku protein and DNA. J Biol Chem 261, 10375-10379. Mimori, T., Akizuki, M., Yamagata, H., Inada, S., Yoshida, S., and Homma, M. (1981). Characterization of a high molecular weight acidic nuclear protein recognized by autoantibodies in sera from patients with polymyositis-scleroderma overlap. J Clin Invest 68, 611-620. Molina, C., and Grotewold, E. (2005). Genome wide analysis of Arabidopsis core promoters. BMC Genomics 6, 25. Morita, A., Umemura, T., Kuroyanagi, M., Futsuhara, Y., Perata, P., and Yamaguchi, J. (1998). Functional dissection of a sugar-repressed alpha-amylase gene (RAmy1 A) promoter in rice embryos. FEBS Lett 423, 81-85. Murashige, T. (1973). Nutrition of plant cells and organs in vitro. In Vitro 9, 81-85. Murashige, T., and Skoog, F. (1962). A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15, 473-479. Nakhamchik, A., Zhao, Z., Provart, N.J., Shiu, S.H., Keatley, S.K., Cameron, R.K., and Goring, D.R. (2004). A comprehensive expression analysis of the Arabidopsis proline-rich extensin-like receptor kinase gene family using bioinformatic and experimental approaches. Plant Cell Physiol 45, 1875-1881. O'Connor, T.R., Dyreson, C., and Wyrick, J.J. (2005). Athena: a resource for rapid visualization and systematic analysis of Arabidopsis promoter sequences. Bioinformatics 21, 4411-4413. Obayashi, T., Kinoshita, K., Nakai, K., Shibaoka, M., Hayashi, S., Saeki, M., Shibata, D., Saito, K., and Ohta, H. (2007). ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Res 35, D863-869. Palaniswamy, S.K., James, S., Sun, H., Lamb, R.S., Davuluri, R.V., and Grotewold, E. (2006). AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks. Plant Physiol 140, 818-829. Pastuglia, M., Roby, D., Dumas, C., and Cock, J.M. (1997). Rapid induction by wounding and bacterial infection of an S gene family receptor-like kinase gene in Brassica oleracea. Plant Cell 9, 49-60. Pimenta Lange, M.J., and Lange, T. (2006). Gibberellin biosynthesis and the regulation of plant development. Plant Biol (Stuttg) 8, 281-290. Poberts, C.S., Rajagopal, S., Smith, L., Nghyen, T., Yang, W., Nugroho, S., Ravi, R.S., Cao, M.L., Chandra, K.V., Pattell, V., Harcourt, R., Dransfield, L., Desamero, N., Slamst, I., Keese, P., Kilian, A., and Jefferson, R.A. (1997). A comprehensive set of modular vectors for advanced manipulation and efficient transformation of plants. Rockefeller Found. Meet. Intern. Program on Rice Biotechnology., 15-19 Sept. Malacca, Malaysia. Ponger, L., and Mouchiroud, D. (2002). CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences. Bioinformatics 18, 631-633. Poole, R.L. (2007). The TAIR Database. Methods Mol Biol 406, 179-212. Pradhan, S., Urwin, N.A., Jenkins, G.I., and Adams, R.L. (1999). Effect of CWG methylation on expression of plant genes. Biochem J 341 ( Pt 3), 473-476. Rasmussen, T.B., and Donaldson, I.A. (2006). Investigation of the endosperm-specific sucrose synthase promoter from rice using transient expression of reporter genes in guar seed tissue. Plant Cell Rep 25, 1035-1042. Razem, F.A., Baron, K., and Hill, R.D. (2006). Turning on gibberellin and abscisic acid signaling. Curr Opin Plant Biol 9, 454-459. Rhee, S.Y., Beavis, W., Berardini, T.Z., Chen, G., Dixon, D., Doyle, A., Garcia-Hernandez, M., Huala, E., Lander, G., Montoya, M., Miller, N., Mueller, L.A., Mundodi, S., Reiser, L., Tacklind, J., Weems, D.C., Wu, Y., Xu, I., Yoo, D., Yoon, J., and Zhang, P. (2003). The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res 31, 224-228. Riano-Pachon, D.M., Ruzicic, S., Dreyer, I., and Mueller-Roeber, B. (2007). PlnTFDB: an integrative plant transcription factor database. BMC Bioinformatics 8, 42. Rieping, M., and Schoffl, F. (1992). Synergistic effect of upstream sequences, CCAAT box elements, and HSE sequences for enhanced expression of chimaeric heat shock genes in transgenic tobacco. Mol Gen Genet 231, 226-232. Riha, K., and Shippen, D.E. (2003). Ku is required for telomeric C-rich strand maintenance but not for end-to-end chromosome fusions in Arabidopsis. Proc Natl Acad Sci U S A 100, 611-615. Riha, K., Watson, J.M., Parkey, J., and Shippen, D.E. (2002). Telomere length deregulation and enhanced sensitivity to genotoxic stress in Arabidopsis mutants deficient in Ku70. Embo J 21, 2819-2826. Rombauts, S., Florquin, K., Lescot, M., Marchal, K., Rouze, P., and van de Peer, Y. (2003). Computational approaches to identify promoters and cis-regulatory elements in plant genomes. Plant Physiol 132, 1162-1176. Rouster, J., Leah, R., Mundy, J., and Cameron-Mills, V. (1997). Identification of a methyl jasmonate-responsive region in the promoter of a lipoxygenase 1 gene expressed in barley grain. Plant J 11, 513-523. Rubio-Somoza, I., Martinez, M., Diaz, I., and Carbonero, P. (2006). HvMCB1, a R1MYB transcription factor from barley with antagonistic regulatory functions during seed development and germination. Plant J 45, 17-30. Sandelin, A., Alkema, W., Engstrom, P., Wasserman, W.W., and Lenhard, B. (2004). JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res 32, D91-94. Schindler, U., Beckmann, H., and Cashmore, A.R. (1992). TGA1 and G-box binding factors: two distinct classes of Arabidopsis leucine zipper proteins compete for the G-box-like element TGACGTGG. Plant Cell 4, 1309-1319. Schug, J., and Overton, G.C. (1997). TESS: Transcription Element Search Software on the WWW (http://www.cbil.upenn.edu/tessTest). Technical Report CBIL-TR-1997-1001-v0.0, Computational Biology and Informatics Laboratory School of Medicine University of Pennsylvania. Shinozaki, K., and Yamaguchi-Shinozaki, K. (1997). Gene expression and signal transduction in water-stress response. Plant Physiol 115, 327-334. Smale, S.T., and Kadonaga, J.T. (2003). The RNA polymerase II core promoter. Annu Rev Biochem 72, 449-479. Smider, V., Rathmell, W.K., Lieber, M.R., and Chu, G. (1994). Restoration of X-ray resistance and V(D)J recombination in mutant cells by Ku cDNA. Science 266, 288-291. Srikant, R., Vu, Q., and Agrawal, R. (1995). Mining generalized association rules. in Proceedings of 21st International Conference on Very Large Databases, 407-419. Steffens, N.O., Galuschka, C., Schindler, M., Bulow, L., and Hehl, R. (2005). AthaMap web tools for database-assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana. Nucleic Acids Res 33, W397-402. Steinhauser, D., Usadel, B., Luedemann, A., Thimm, O., and Kopka, J. (2004). CSB.DB: a comprehensive systems-biology database. Bioinformatics 20, 3647-3651. Swarbreck, D., Wilks, C., Lamesch, P., Berardini, T.Z., Garcia-Hernandez, M., Foerster, H., Li, D., Meyer, T., Muller, R., Ploetz, L., Radenbaugh, A., Singh, S., Swing, V., Tissier, C., Zhang, P., and Huala, E. (2008). The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res 36, D1009-1014. Takai, D., and Jones, P.A. (2003). The CpG island searcher: a new WWW resource. In Silico Biol 3, 235-240. Tamura, K., Adachi, Y., Chiba, K., Oguchi, K., and Takahashi, H. (2002). Identification of Ku70 and Ku80 homologues in Arabidopsis thaliana: evidence for a role in the repair of DNA double-strand breaks. Plant J 29, 771-781. Tatematsu, K., Ward, S., Leyser, O., Kamiya, Y., and Nambara, E. (2005). Identification of cis-elements that regulate gene expression during initiation of axillary bud outgrowth in Arabidopsis. Plant Physiol 138, 757-766. Tatusova, T.A., and Madden, T.L. (1999). BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 174, 247-250. Teale, W.D., Paponov, I.A., and Palme, K. (2006). Auxin in action: signalling, transport and the control of plant growth and development. Nat Rev Mol Cell Biol 7, 847-859. Toufighi, K., Brady, S.M., Austin, R., Ly, E., and Provart, N.J. (2005). The Botany Array Resource: e-Northerns, Expression Angling, and promoter analyses. Plant J 43, 153-163. Tran, R.K., Henikoff, J.G., Zilberman, D., Ditt, R.F., Jacobsen, S.E., and Henikoff, S. (2005). DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Curr Biol 15, 154-159. Tuteja, N., Tuteja, R., Ochem, A., Taneja, P., Huang, N.W., Simoncsits, A., Susic, S., Rahman, K., Marusic, L., and Chen, J. (1994). Human DNA helicase II: a novel DNA unwinding enzyme identified as the Ku autoantigen. Embo J 13, 4991-5001. Tuteja, R., and Tuteja, N. (2000). Ku autoantigen: a multifunctional DNA-binding protein. Crit Rev Biochem Mol Biol 35, 1-33. Ulmasov, T., Hagen, G., and Guilfoyle, T.J. (1999). Activation and repression of transcription by auxin-response factors. Proc Natl Acad Sci U S A 96, 5844-5849. Vaucheret, H., and Fagard, M. (2001). Transcriptional gene silencing in plants: targets, inducers and regulators. Trends Genet 17, 29-35. Vieten, A., Sauer, M., Brewer, P.B., and Friml, J. (2007). Molecular and cellular aspects of auxin-transport-mediated development. Trends Plant Sci 12, 160-168. Vlieghe, D., Sandelin, A., De Bleser, P.J., Vleminckx, K., Wasserman, W.W., van Roy, F., and Lenhard, B. (2006). A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. Nucleic Acids Res 34, D95-97. Wasternack, C., Stenzel, I., Hause, B., Hause, G., Kutter, C., Maucher, H., Neumerkel, J., Feussner, I., and Miersch, O. (2006). The wound response in tomato--role of jasmonic acid. J Plant Physiol 163, 297-306. Wellmer, F., Alves-Ferreira, M., Dubois, A., Riechmann, J.L., and Meyerowitz, E.M. (2006). Genome-wide analysis of gene expression during early Arabidopsis flower development. PLoS Genet 2, e117. West, C.E., Waterworth, W.M., Story, G.W., Sunderland, P.A., Jiang, Q., and Bray, C.M. (2002). Disruption of the Arabidopsis AtKu80 gene demonstrates an essential role for AtKu80 protein in efficient repair of DNA double-strand breaks in vivo. Plant J 31, 517-528. Wingender, E., Karas, H., and Knuppel, R. (1997). TRANSFAC database as a bridge between sequence data libraries and biological function. Pac Symp Biocomput, 477-485. Wingender, E., Chen, X., Hehl, R., Karas, H., Liebich, I., Matys, V., Meinhardt, T., Pruss, M., Reuter, I., and Schacherer, F. (2000). TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res 28, 316-319. Winter, D., Vinegar, B., Nahal, H., Ammar, R., Wilson, G.V., and Provart, N.J. (2007). An "electronic fluorescent pictograph" browser for exploring and analyzing large-scale biological data sets. PLoS ONE 2, e718. Wray, G.A., Hahn, M.W., Abouheif, E., Balhoff, J.P., Pizer, M., Rockman, M.V., and Romano, L.A. (2003). The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol 20, 1377-1419. Yamada, K., Lim, J., Dale, J.M., Chen, H., Shinn, P., Palm, C.J., Southwick, A.M., Wu, H.C., Kim, C., Nguyen, M., Pham, P., Cheuk, R., Karlin-Newmann, G., Liu, S.X., Lam, B., Sakano, H., Wu, T., Yu, G., Miranda, M., Quach, H.L., Tripp, M., Chang, C.H., Lee, J.M., Toriumi, M., Chan, M.M., Tang, C.C., Onodera, C.S., Deng, J.M., Akiyama, K., Ansari, Y., Arakawa, T., Banh, J., Banno, F., Bowser, L., Brooks, S., Carninci, P., Chao, Q., Choy, N., Enju, A., Goldsmith, A.D., Gurjal, M., Hansen, N.F., Hayashizaki, Y., Johnson-Hopson, C., Hsuan, V.W., Iida, K., Karnes, M., Khan, S., Koesema, E., Ishida, J., Jiang, P.X., Jones, T., Kawai, J., Kamiya, A., Meyers, C., Nakajima, M., Narusaka, M., Seki, M., Sakurai, T., Satou, M., Tamse, R., Vaysberg, M., Wallender, E.K., Wong, C., Yamamura, Y., Yuan, S., Shinozaki, K., Davis, R.W., Theologis, A., and Ecker, J.R. (2003). Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302, 842-846. Yamaguchi-Shinozaki, K., and Shinozaki, K. (1994). A novel cis-acting element in an Arabidopsis gene is involved in responsiveness to drought, low-temperature, or high-salt stress. Plant Cell 6, 251-264. Yan, K.H., Liu, P.F., Tzeng, H.T., Chang, W.C., Chou, W.G., and Pan, R.L. (2004). Characterization of DNA end-binding activities in higher plants. Plant Physiol Biochem 42, 617-622. Yoo, S., and Dynan, W.S. (1998). Characterization of the RNA binding properties of Ku protein. Biochemistry 37, 1336-1343. Yu, X., Lin, J., Masuda, T., Esumi, N., Zack, D.J., and Qian, J. (2006). Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae. Nucleic Acids Res 34, 917-927. Yuan, Q., Ouyang, S., Wang, A., Zhu, W., Maiti, R., Lin, H., Hamilton, J., Haas, B., Sultana, R., Cheung, F., Wortman, J., and Buell, C.R. (2005). The institute for genomic research Osa1 rice genome annotation database. Plant Physiol 138, 18-26. Zelazowski, P., Max, E.E., Kehry, M.R., and Snapper, C.M. (1997). Regulation of Ku expression in normal murine B cells by stimuli that promote switch recombination. J Immunol 159, 2559-2562. Zemach, A., and Grafi, G. (2007). Methyl-CpG-binding domain proteins in plants: interpreters of DNA methylation. Trends Plant Sci. Zhu, Q.H., Guo, A.Y., Gao, G., Zhong, Y.F., Xu, M., Huang, M., and Luo, J. (2007). DPTF: a database of poplar transcription factors. Bioinformatics 23, 1307-1308. Zimmermann, P., Hirsch-Hoffmann, M., Hennig, L., and Gruissem, W. (2004). GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol 136, 2621-2632.; http://nthur.lib.nthu.edu.tw/dspace/handle/987654321/31684Test
الإتاحة: http://nthur.lib.nthu.edu.tw/dspace/handle/987654321/31684Test
رقم الانضمام: edsbas.D7F5AA12
قاعدة البيانات: BASE